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authorThomas White <taw@physics.org>2010-01-22 15:50:41 +0100
committerThomas White <taw@physics.org>2010-01-22 15:50:41 +0100
commit75d30a3f2a7d8484575f5b6ba6ed07587dc19f1e (patch)
tree58c78fbccd5544eabe7d8484fbaf6358ed87327d /src
parentef9281fb30a07b8ee099ada3e1f7a0a10cbca5c0 (diff)
Add --near-bragg and --simulate options to indexamajig
Diffstat (limited to 'src')
-rw-r--r--src/Makefile.am3
-rw-r--r--src/diffraction.c4
-rw-r--r--src/indexamajig.c46
3 files changed, 46 insertions, 7 deletions
diff --git a/src/Makefile.am b/src/Makefile.am
index 57ee19c4..a80ba7a2 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -17,7 +17,8 @@ process_hkl_SOURCES = process_hkl.c sfac.c statistics.c cell.c utils.c \
process_hkl_LDADD = @LIBS@
indexamajig_SOURCES = indexamajig.c hdf5-file.c utils.c dirax.c cell.c image.c \
- intensities.c ewald.c peaks.c index.c filters.c
+ intensities.c ewald.c peaks.c index.c filters.c \
+ diffraction.c detector.c sfac.c
indexamajig_LDADD = @LIBS@
if HAVE_GTK
diff --git a/src/diffraction.c b/src/diffraction.c
index a0248450..b7bdb75a 100644
--- a/src/diffraction.c
+++ b/src/diffraction.c
@@ -142,7 +142,9 @@ void get_diffraction(struct image *image, int na, int nb, int nc)
double a, b, c, d;
/* Generate the array of reciprocal space vectors in image->qvecs */
- get_ewald(image);
+ if ( image->qvecs == NULL ) {
+ get_ewald(image);
+ }
if ( image->molecule == NULL ) {
image->molecule = load_molecule();
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 68b39c20..3142b748 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -28,6 +28,8 @@
#include "intensities.h"
#include "ewald.h"
#include "peaks.h"
+#include "diffraction.h"
+#include "detector.h"
static void show_help(const char *s)
@@ -45,6 +47,9 @@ static void show_help(const char *s)
" don't actually index.\n"
" --dirax Use DirAx for indexing.\n"
" --dump-peaks Write the results of the peak search to stdout.\n"
+" --near-bragg Output a list of reflection intensities to stdout.\n"
+" --simulate Simulate the diffraction pattern using the indexed\n"
+" unit cell.\n"
"\n");
}
@@ -60,6 +65,8 @@ int main(int argc, char *argv[])
int config_noindex = 0;
int config_dumpfound = 0;
int config_dirax = 0;
+ int config_nearbragg = 0;
+ int config_simulate = 0;
/* Long options */
const struct option longopts[] = {
@@ -67,7 +74,9 @@ int main(int argc, char *argv[])
{"input", 1, NULL, 'i'},
{"no-index", 0, &config_noindex, 1},
{"dump-peaks", 0, &config_dumpfound, 1},
+ {"near-bragg", 0, &config_nearbragg, 1},
{"dirax", 0, &config_dirax, 1},
+ {"simulate", 0, &config_simulate, 1},
{0, 0, NULL, 0}
};
@@ -149,13 +158,16 @@ int main(int argc, char *argv[])
if ( config_dumpfound ) dump_peaks(&image);
- if ( !config_noindex ) {
+ /* Not indexing? Then there's nothing left to do. */
+ if ( config_noindex ) goto done;
- /* Calculate orientation matrix (by magic) */
- index_pattern(&image, config_noindex,
- config_dirax);
+ /* Calculate orientation matrix (by magic) */
+ index_pattern(&image, config_noindex,
+ config_dirax);
- if ( image.molecule == NULL ) goto done;
+ if ( image.molecule == NULL ) goto done;
+
+ if ( config_nearbragg || config_simulate ) {
/* View head-on (unit cell is tilted) */
image.orientation.w = 1.0;
@@ -164,10 +176,34 @@ int main(int argc, char *argv[])
image.orientation.z = 0.0;
get_ewald(&image);
+ }
+
+ if ( config_nearbragg ) {
/* Read h,k,l,I */
output_intensities(&image);
}
+ if ( config_simulate ) {
+
+ /* Simulate a diffraction pattern */
+ image.sfacs = NULL;
+ image.data = NULL;
+ image.twotheta = NULL;
+ image.hdr = NULL;
+ image.molecule = NULL;
+
+ get_diffraction(&image, 8, 8, 8);
+ if ( image.molecule == NULL ) {
+ ERROR("Couldn't open molecule.pdb\n");
+ return 1;
+ }
+ record_image(&image, 0, 0, 0);
+
+ hdf5_write("simulated.h5", image.data,
+ image.width, image.height);
+
+ }
+
}
done: